A powerful lobbying organisation representing agribusiness interests helped draft a key government report that has been attacked by environmentalists for heavily favouring the arguments of the genetically modified food industry.

The revelation comes after the resignation of two government advisers who have criticised the close relationship between the Food Standards Agency (FSA), the body that oversees the UK's food industry, and the GM lobby.

Emails between the FSA and the Agricultural Biotechnology Council (ABC) show the council inserted key sentences strengthening the case for GM food that ended up in the final report.

Emails from the council – which represents leading GM food companies such as Monsanto and Bayer – to Dr Clair Baynton, the then head of novel foods at the FSA, show a close dialogue between both sides between 2008 and August 2009, when the report was published.

On 19 November 2008, Baynton sent the council a draft of the report, saying: "I am happy to discuss… if that would be helpful."

In response, the council suggested a series of changes that emphasised how GM food was playing an increasingly important role in global agriculture and helping bring down food prices. Some of the amendments were rejected by the FSA, but others were accepted.

One accepted alteration acknowledged the GM lobby's argument that GM food is inevitable in the European Union because of its ubiquity elsewhere. It stated that "retailers were concerned they may not be able to maintain their current non-GM sources of supply as producers increasingly adopt GM technology around the world".

And the FSA also accepted the suggested amendment that soya protein (which can be grown as a GM crop) remains "the most cost-effective method of supplementing animal feed at present". Baynton replied a few days later: "Many thanks for your comments on the draft report", and asked the council for help in finding evidence of the prevalence of GM foods, "either authorised or being considered for authorisation in Argentina, Brazil and the US".

Months later, the council sent Baynton, a former employee of GM food producer Syngenta, a list of whom it wanted on a steering group overseeing a "public engagement exercise" on GM food. The email stated: "We believe GM must be presented as an option within the wider context of food security as part of a solution to feeding a growing population."

The FSA was due to start the public engagement exercise, which is expected to cost the taxpayer £500,000, this month. But the move is being seen in some quarters as a "rigged" exercise.

Two members who sit on the FSA's steering group have resigned in protest. Dr Helen Wallace, director of Genewatch UK, a scientific pressure group opposed to GM, stepped down last month. Last week, the group's vice-chairman, Professor Brian Wynne, an expert on public engagement with science, resigned, complaining that the FSA had adopted a "dogmatically entrenched", pro-GM attitude.

Wallace said the emails "expose how the Food Standards Agency is acting as a puppet of the GM industry, by colluding with foreign GM companies to undermine people's access to GM-free food supplies in Britain". The FSA is chaired by former Labour minister Lord Rooker, a GM enthusiast, who has attacked its critics as "anti-science".

A confidential bid document to win the contract to run the engagement exercise, submitted by the polling company Ipsos MORI, acknowledges the sensitivity of the initiative. "There will be no active seeking of media interest in relation to this project," it explains.

The bidding document states that it works on behalf of a "multinational agro-chemical and seed company" and warns: "Campaign organisations who may feel that the 'battle' was won in 2003 could decide to try and hijack the process to ensure GM food does not get a chance to be reintroduced into the UK."

An FSA spokesman defended its decision to include the GM lobby's suggested changes in the final report.

"In order to obtain an accurate picture of the situation, the FSA held a series of meetings with stakeholders before drafting this report," the spokesman said. "As the report was concerned with the markets for food and animal feed, the biotech industry had not been involved in these meetings. However, in order to ensure the report was balanced and not to exclude this relevant stakeholder group, the view of the ABC was also sought. Their comments were taken on board in the final draft, as were the comments by other stakeholders."

But Wallace was critical of the decision. "The stakeholder meeting was transparent – the changes made behind the scenes at the industry's request were not," she said. "The report fails to represent the vast majority of GM-free farmers, who will have to pay a heavy price if their crops or seed are allowed to become contaminated with GM crops or seed."

The row came as the environment secretary, Caroline Spelman, who used to work as director of a biotech lobbying firm, said that she was in favour of GM foods "in the right circumstances".